`pyqmmm.md.amber_toolkit`¶

A library of CPPTraj scripts and built-in generator functions.

Module Contents¶

`get_last_frame`(prmtop, mdcrd, output_pdb)	Get the last frame from a trajectory as a PDB.
`run_cpptraj`(cpptraj_script[, script_name])	A generalizable function that can be used to run any of the cpptraj scripts.
`submit_script`(protein_id, script_name, cpus)	Classic submit script for CPPTraj jobs.
`calculate_hbonds_script`(protein_id, substrate_index, ...)	Calculate all hbonds that form between the protein and substrate.
`closest_waters_script`(protein_id, centroid, all_residues)	Extract the 9000 waters closest to the centroid
`strip_all_script`(protein_id)	Strip waters, ions, and metals and generate new mdcrd and prmtop files
`basic_metrics_script`(protein_id, all_residues, ...)	Get basic useful metrics
`angles_and_dist_script`(protein_id, h_index, oxo_index, ...)	Get distances and angles
`gbsa_script`(protein_id, ligand_name, ligand_index, ...)	Submit a GBSA calculation.

pyqmmm.md.amber_toolkit.get_last_frame(prmtop, mdcrd, output_pdb)[source]¶

Get the last frame from a trajectory as a PDB.

Parameters:

pyqmmm.md.amber_toolkit.run_cpptraj(cpptraj_script, script_name='cpptraj_script.in')[source]¶

A generalizable function that can be used to run any of the cpptraj scripts.

This script will submit the job interactively rather than as a queued job. It would not be a good idea to use this script with a long job.

Parameters:

cpptraj_script (str) – The content of the CPPTRAJ script as a string
script_name (str, optional) – The name of the script file (default is “cpptraj_script.in”)

pyqmmm.md.amber_toolkit.submit_script(protein_id, script_name, cpus)[source]¶

Classic submit script for CPPTraj jobs.

This script is for Gibraltar but can be modified for any SGE system.

pyqmmm.md.amber_toolkit.calculate_hbonds_script(protein_id, substrate_index, residue_range)[source]¶: Calculate all hbonds that form between the protein and substrate.

pyqmmm.md.amber_toolkit.closest_waters_script(protein_id, centroid, all_residues)[source]¶: Extract the 9000 waters closest to the centroid

pyqmmm.md.amber_toolkit.strip_all_script(protein_id)[source]¶: Strip waters, ions, and metals and generate new mdcrd and prmtop files

pyqmmm.md.amber_toolkit.basic_metrics_script(protein_id, all_residues, select_residues)[source]¶: Get basic useful metrics

pyqmmm.md.amber_toolkit.angles_and_dist_script(protein_id, h_index, oxo_index, iron_index)[source]¶: Get distances and angles

pyqmmm.md.amber_toolkit.gbsa_script(protein_id, ligand_name, ligand_index, start, stride, cpus=16)[source]¶

Submit a GBSA calculation.

Parameters:

protein_id (str) – The name of the protein (e.g., taud, mc6, besd)
ligand_name (str) – The name of the ligand (e.g, tau, hm1)
ligand_index (int) – The index of the ligand, except subtract one if it comes after the metal
start (int) – What frame to start the mmGBSA calculation on
stride (int) – Every how many frames
cpus (int) – How many cpus to employ, 16 may be a good number